What games impressed you with their graphics on release, but you think look terrible in hindsight? 

Mortal Kombat- The mocap stuff was nifty at the time, but sprites aged much better.
FF7- The out of battle character models are kind of ugly. Sort of ugly in a charming bulldog kind of way, but ugly nevertheless.
Skyward Sword- Not quite ugly but I originally played this on a 480p TV and it looked good. When you try it on a larger higher resolution TV the flaws become much more noticeable.

Super Mario 64

Outcast

Pretty much everything on PS1/N64/Saturn. Although they can be improved with uprising the graphics and tweaking them a bit like all the games on Rare Replay and recent games like Doom 64 and Turok. Final Fantasy 7 and Chrono Cross come to mind for my answer.

Yeah, other than a few 2D games, and games that made heavy use of alphamaps (like FF Tactics) that generation hasn't really aged well. :P

pong

Forgot about Virtua Racing on the Genesis. 

That Trevellyan comes straight from the uncanny valley. The realistic face plastered on the low polygon body...

Lol, I chose that screenshot just for that ridiculous Uncanny Valley look! :D